Class II MHC (Ia) gene products play critical roles in a variety of T lymphocyte responses. A combination of immunological, molecular genetic, and biochemical approaches is being used to study the relationship between Ia structure and function. Ia expression has been examined following transfer of class II genes into a variety of recipient cells. These experiments have shown that polymorphic regions of the Ia molecule play a critical role in regulating membrane expression. For the beta chain, irrespective of the alpha chain origin, allelically variable residues in the amino-terminal 50 amino acids control the level of surface expression. This control primarily affects the efficiency of transport, not the initial pairing of the chains. Invariant chain (li) is not required for this transport event. Dissection of Ia structure-function relationships has revealed a segmental structure for these molecules. Distinct variable subregions participate differently in either control of expression, binding and display of antigenic peptides, or interaction with the T cell receptor. In particular, a single amino-acid change at position 29 in the E beta chain alters the presentation of pigeon cytochrome c without affecting general properties of T cell recognition of the I-E molecule. Changes in positions 67, 70, or 71 of the A beta chain, however, affect almost all T cell responses to the I-A molecule. The cell biology of antigen processing and presentation by MHC molecules has been studied and a special role for the endosome/trans-Golgi low pH compartments demonstrated. The rules controlling class I vs class II MHC antigen presentation have been examined, with the data indicating that the way antigen enters a cell may determine the class of MHC molecule used for presentation. These studies are providing new insight into the rules governing T cell co-recognition of antigen and MHC molecules, and the biochemistry and cell biology of protein multimer synthesis and transport.